86 results found
Martín AFM, Pérez ZMC, 2021, Discussion "COVID-19 and pandemics in history", Historia y Memoria, ISSN: 2027-5137
España G, Cucunubá ZM, Cuervo-Rojas J, et al., 2021, The potential impact of delta variant of SARS-CoV-2 in the context of limited vaccination coverage and increasing social mixing in Bogotá, Colombia
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>More than 122,000 COVID-19 associated deaths have been reported in Colombia and about 27,000 in the city of Bogotá by the first week of August, with vaccination coverage in the city at 30% for complete schemes and at 37% for partial vaccination. As the incidence of cases currently decreases, questions remain about the potential impact of the delta variant already present in the city.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We used an agent-based model calibrated to data on age-structured deaths and dominance of variants in Bogotá. We used efficacy data for the portfolio of vaccines available, including known changes for SARS-CoV-2 variants. We modelled scenarios of early and delayed introduction of the delta variant in the city along with changes in mobility and social contact, and vaccine strategies over the next months.</jats:p></jats:sec><jats:sec><jats:title>Findings</jats:title><jats:p>We estimate that by mid July, vaccination may have already prevented 17,800 (95% CrI: 16,000 - 19,000) deaths in Bogotá. The delta variant could become dominant and lead to a fourth wave later in the year, but its timing will depend on the date of introduction, social mixing patterns, and vaccination strategy. In all scenarios, higher social mixing is associated with a fourth wave of considerable magnitude. If an early delta introduction occurred (dominance by mid July), a new wave may occur in August/September and in such case, age prioritization of vaccination and second dose not postponed are more important. However, if introduction occurred one or two months later (dominance by mid August/September) the age-prioritization is less relevant but maintaining the dose scheme without postponement is more important. In all scenarios we found t
Clark J, Stolk WA, Basáñez M-G, et al., 2021, How modelling can help steer the course set by the World Health Organization 2021-2030 roadmap on neglected tropical diseases, Gates Open Research, Vol: 5, Pages: 112-112
<ns3:p>The World Health Organization recently launched its 2021-2030 roadmap, <ns3:italic>Ending</ns3:italic><ns3:italic> the </ns3:italic><ns3:italic>Neglect</ns3:italic><ns3:italic> to </ns3:italic><ns3:italic>Attain</ns3:italic><ns3:italic> the </ns3:italic><ns3:italic>Sustainable Development Goals</ns3:italic><ns3:italic>,</ns3:italic> an updated call to arms to end the suffering caused by neglected tropical diseases. Modelling and quantitative analyses played a significant role in forming these latest goals. In this collection, we discuss the insights, the resulting recommendations and identified challenges of public health modelling for 13 of the target diseases: Chagas disease, dengue, <ns3:italic>gambiense</ns3:italic> human African trypanosomiasis (gHAT), lymphatic filariasis (LF), onchocerciasis, rabies, scabies, schistosomiasis, soil-transmitted helminthiases (STH), <ns3:italic>Taenia solium</ns3:italic> taeniasis/ cysticercosis, trachoma, visceral leishmaniasis (VL) and yaws. This piece reflects the three cross-cutting themes identified across the collection, regarding the contribution that modelling can make to timelines, programme design, drug development and clinical trials.</ns3:p>
Charniga K, Cucunuba ZM, Mercado M, et al., 2021, Spatial and temporal invasion dynamics of the 2014-2017 Zika and chikungunya epidemics in Colombia, PLOS COMPUTATIONAL BIOLOGY, Vol: 17, ISSN: 1553-734X
Caicedo Y, Charniga K, Rueda A, et al., 2021, The epidemiology of Mayaro virus in the Americas: a systematic review and key parameter estimates for outbreak modelling, PLoS Neglected Tropical Diseases, Vol: 15, ISSN: 1935-2727
Mayaro virus (MAYV) is an arbovirus that is endemic to tropical forests in Central and South America, particularly within the Amazon basin. In recent years, concern has increased regarding MAYV’s ability to invade urban areas and cause epidemics across the region. We conducted a systematic literature review to characterise the evolutionary history of MAYV, its transmission potential, and exposure patterns to the virus. We analysed data from the literature on MAYV infection to produce estimates of key epidemiological parameters, including the generation time and the basic reproduction number, R0. We also estimated the force-of-infection (FOI) in epidemic and endemic settings. Seventy-six publications met our inclusion criteria. Evidence of MAYV infection in humans, animals, or vectors was reported in 14 Latin American countries. Nine countries reported evidence of acute infection in humans confirmed by viral isolation or reverse transcription-PCR (RT-PCR). We identified at least five MAYV outbreaks. Seroprevalence from population based cross-sectional studies ranged from 21% to 72%. The estimated mean generation time of MAYV was 15.2 days (95% CrI: 11.7–19.8) with a standard deviation of 6.3 days (95% CrI: 4.2–9.5). The per-capita risk of MAYV infection (FOI) ranged between 0.01 and 0.05 per year. The mean R0 estimates ranged between 2.1 and 2.9 in the Amazon basin areas and between 1.1 and 1.3 in the regions outside of the Amazon basin. Although MAYV has been identified in urban vectors, there is not yet evidence of sustained urban transmission. MAYV’s enzootic cycle could become established in forested areas within cities similar to yellow fever virus.
Ragonnet-Cronin M, Boyd O, Geidelberg L, et al., 2021, Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions, Nature Communications, Vol: 12, Pages: 1-7, ISSN: 2041-1723
Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non- pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were examined in relation to the dates of the most stringent interventions in each location as well as to the number of cumulative COVID-19 deaths and phylodynamic estimates of epidemic size. Here we report that the time elapsed between epidemic origin and maximum intervention is associated with different measures of epidemic severity and explains 11% of the variance in reported deaths one month after the most stringent intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced 30 much less severe COVID-19 morbidity and mortality during the period of study.
Vecino-Ortiz AI, Villanueva Congote J, Zapata Bedoya S, et al., 2021, Impact of contact tracing on COVID-19 mortality: an impact evaluation using surveillance data from Colombia, PLoS One, Vol: 16, ISSN: 1932-6203
BACKGROUND: Contact tracing is a crucial part of the public health surveillance toolkit. However, it is labor-intensive and costly to carry it out. Some countries have faced challenges implementing contact tracing, and no impact evaluations using empirical data have assessed its impact on COVID-19 mortality. This study assesses the impact of contact tracing in a middle-income country, providing data to support the expansion and optimization of contact tracing strategies to improve infection control. METHODS: We obtained publicly available data on all confirmed COVID-19 cases in Colombia between March 2 and June 16, 2020. (N = 54,931 cases over 135 days of observation). As suggested by WHO guidelines, we proxied contact tracing performance as the proportion of cases identified through contact tracing out of all cases identified. We calculated the daily proportion of cases identified through contact tracing across 37 geographical units (32 departments and five districts). Further, we used a sequential log-log fixed-effects model to estimate the 21-days, 28-days, 42-days, and 56-days lagged impact of the proportion of cases identified through contact tracing on daily COVID-19 mortality. Both the proportion of cases identified through contact tracing and the daily number of COVID-19 deaths are smoothed using 7-day moving averages. Models control for the prevalence of active cases, second-degree polynomials, and mobility indices. Robustness checks to include supply-side variables were performed. RESULTS: We found that a 10 percent increase in the proportion of cases identified through contact tracing is related to COVID-19 mortality reductions between 0.8% and 3.4%. Our models explain between 47%-70% of the variance in mortality. Results are robust to changes of specification and inclusion of supply-side variables. CONCLUSION: Contact tracing is instrumental in containing infectious diseases. Its prioritization as a surveillance strategy will substantially impact reducin
In response to the COVID-19 pandemic, countries have sought to control SARS-CoV-2 transmission by restricting population movement through social distancing interventions, thus reducing the number of contacts.Mobility data represent an important proxy measure of social distancing, and here, we characterise the relationship between transmission and mobility for 52 countries around the world.Transmission significantly decreased with the initial reduction in mobility in 73% of the countries analysed, but we found evidence of decoupling of transmission and mobility following the relaxation of strict control measures for 80% of countries. For the majority of countries, mobility explained a substantial proportion of the variation in transmissibility (median adjusted R-squared: 48%, interquartile range - IQR - across countries [27-77%]). Where a change in the relationship occurred, predictive ability decreased after the relaxation; from a median adjusted R-squared of 74% (IQR across countries [49-91%]) pre-relaxation, to a median adjusted R-squared of 30% (IQR across countries [12-48%]) post-relaxation.In countries with a clear relationship between mobility and transmission both before and after strict control measures were relaxed, mobility was associated with lower transmission rates after control measures were relaxed indicating that the beneficial effects of ongoing social distancing behaviours were substantial.
Sabino EC, Buss LF, Carvalho MPS, et al., 2021, Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence, LANCET, Vol: 397, Pages: 452-455, ISSN: 0140-6736
Li X, Mukandavire C, Cucunuba ZM, et al., 2021, Estimating the health impact of vaccination against ten pathogens in 98 low-income and middle-income countries from 2000 to 2030: a modelling study, The Lancet, Vol: 397, Pages: 398-408, ISSN: 0140-6736
BackgroundThe past two decades have seen expansion of childhood vaccination programmes in low-income and middle-income countries (LMICs). We quantify the health impact of these programmes by estimating the deaths and disability-adjusted life-years (DALYs) averted by vaccination against ten pathogens in 98 LMICs between 2000 and 2030.Methods16 independent research groups provided model-based disease burden estimates under a range of vaccination coverage scenarios for ten pathogens: hepatitis B virus, Haemophilus influenzae type B, human papillomavirus, Japanese encephalitis, measles, Neisseria meningitidis serogroup A, Streptococcus pneumoniae, rotavirus, rubella, and yellow fever. Using standardised demographic data and vaccine coverage, the impact of vaccination programmes was determined by comparing model estimates from a no-vaccination counterfactual scenario with those from a reported and projected vaccination scenario. We present deaths and DALYs averted between 2000 and 2030 by calendar year and by annual birth cohort.FindingsWe estimate that vaccination of the ten selected pathogens will have averted 69 million (95% credible interval 52–88) deaths between 2000 and 2030, of which 37 million (30–48) were averted between 2000 and 2019. From 2000 to 2019, this represents a 45% (36–58) reduction in deaths compared with the counterfactual scenario of no vaccination. Most of this impact is concentrated in a reduction in mortality among children younger than 5 years (57% reduction [52–66]), most notably from measles. Over the lifetime of birth cohorts born between 2000 and 2030, we predict that 120 million (93–150) deaths will be averted by vaccination, of which 58 million (39–76) are due to measles vaccination and 38 million (25–52) are due to hepatitis B vaccination. We estimate that increases in vaccine coverage and introductions of additional vaccines will result in a 72% (59–81) reduction in lifetime mortality in t
Pardo CF, Zapata-Bedoya S, Ramirez-Varela A, et al., 2021, COVID-19 and public transport: an overview and recommendations applicable to Latin America, Infectio, Vol: 25, Pages: 182-182
Fu H, Wang H, Xi X, et al., 2021, A database for the epidemic trends and control measures during the first wave of COVID-19 in mainland China, International Journal of Infectious Diseases, Vol: 102, Pages: 463-471, ISSN: 1201-9712
Objectives: This data collation effort aims to provide a comprehensive database to describe the epidemic trends and responses during the first wave of coronavirus disease 2019 (COVID-19)across main provinces in China. Methods: From mid-January to March 2020, we extracted publicly available data on the spread and control of COVID-19 from 31 provincial health authorities and major media outlets in mainland China. Based on these data, we conducted a descriptive analysis of the epidemics in the six most-affected provinces. Results: School closures, travel restrictions, community-level lockdown, and contact tracing were introduced concurrently around late January but subsequent epidemic trends were different across provinces. Compared to Hubei, the other five most-affected provinces reported a lower crude case fatality ratio and proportion of critical and severe hospitalised cases. From March 2020, as local transmission of COVID-19 declined, switching the focus of measures to testing and quarantine of inbound travellers could help to sustain the control of the epidemic. Conclusions: Aggregated indicators of case notifications and severity distributions are essential for monitoring an epidemic. A publicly available database with these indicators and information on control measures provides useful source for exploring further research and policy planning for response to the COVID-19 epidemic.
Eggo RM, Dawa J, Kucharski AJ, et al., 2021, The importance of local context in COVID-19 models, Nature Computational Science, Vol: 1, Pages: 6-8
Caicedo E-Y, Charniga K, Rueda A, et al., 2020, The epidemiology of Mayaro virus in the Americas: A systematic review and key parameter estimates for outbreak modelling, Publisher: Public Library of Science
<jats:title>Abstract</jats:title><jats:p>Mayaro virus (MAYV) is an arbovirus that is endemic to tropical forests in Central and South America, particularly within the Amazon basin. In recent years, concern has increased regarding MAYV’s ability to invade urban areas and cause epidemics across the region. We conducted a systematic literature review to characterise the evolutionary history of MAYV, its transmission potential, and exposure patterns to the virus. We analysed data from the literature on MAYV infection to produce estimates of key epidemiological parameters, including the generation time and the basic reproduction number, <jats:italic>R</jats:italic><jats:sub>0</jats:sub>. We also estimated the force-of-infection (FOI) in epidemic and endemic settings. Seventy-six publications met our inclusion criteria. Evidence of MAYV infection in humans, animals, or vectors was reported in 14 Latin American countries. Nine countries reported evidence of acute infection in humans confirmed by viral isolation or reverse transcription-PCR (RT-PCR). We identified at least five MAYV outbreaks. Seroprevalence from population based cross-sectional studies ranged from 21% to 72%. The estimated mean generation time of MAYV was 15.2 days (95% CrI: 11.7-19.8) with a standard deviation of 6.3 days (95% CrI: 4.2-9.5). The per-capita risk of MAYV infection (FOI) ranged between 0.01 and 0.05 per year, producing <jats:italic>R</jats:italic><jats:sub>0</jats:sub> estimates between 1.1 and 2.9 in endemic settings. In an outbreak in Santa Cruz, Bolivia, <jats:italic>R</jats:italic><jats:sub>0</jats:sub> was estimated at 2.2 (95% CrI: 0.8-4.8). Although MAYV has been identified in urban vectors, there is not yet evidence of sustained urban transmission. MAYV’s enzootic cycle could become established in forested areas within cities similar to yellow fever virus.</jats:p><jats:sec&
Unwin H, Mishra S, Bradley V, et al., 2020, State-level tracking of COVID-19 in the United States, Nature Communications, Vol: 11, Pages: 1-9, ISSN: 2041-1723
As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, using publicly available deathdata within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We use changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on therate of transmission of SARS-CoV-2. We estimate thatRtwas only below one in 23 states on 1st June. We also estimate that 3.7% [3.4%-4.0%] of the total population of the US had been infected, with wide variation between states, and approximately 0.01% of the population was infectious. We demonstrate good 3 week model forecasts of deaths with low error and good coverage of our credible intervals.
Laiton-Donato K, Julian Villabona-Arenas C, Usme-Ciro JA, et al., 2020, Genomic epidemiology of severe acute respiratory syndrome Coronavirus 2, Colombia, Emerging Infectious Diseases, Vol: 26, Pages: 2854-2862, ISSN: 1080-6040
Coronavirus disease (COVID-19) in Colombia was first diagnosed in a traveler arriving from Italy on February 26, 2020. However, limited data are available on the origins and number of introductions of COVID-19 into the country. We sequenced the causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), from 43 clinical samples we collected, along with another 79 genome sequences available from Colombia. We investigated the emergence and importation routes for SARS-CoV-2 into Colombia by using epidemiologic, historical air travel, and phylogenetic observations. Our study provides evidence of multiple introductions, mostly from Europe, and documents >12 lineages. Phylogenetic findings validate the lineage diversity, support multiple importation events, and demonstrate the evolutionary relationship of epidemiologically linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigations.
Grassly NC, Pons-Salort M, Parker EPK, et al., 2020, Comparison of molecular testing strategies for COVID-19 control: a mathematical modelling study, Lancet Infectious Diseases, Vol: 20, Pages: 1381-1389, ISSN: 1473-3099
BACKGROUND: WHO has called for increased testing in response to the COVID-19 pandemic, but countries have taken different approaches and the effectiveness of alternative strategies is unknown. We aimed to investigate the potential impact of different testing and isolation strategies on transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: We developed a mathematical model of SARS-CoV-2 transmission based on infectiousness and PCR test sensitivity over time since infection. We estimated the reduction in the effective reproduction number (R) achieved by testing and isolating symptomatic individuals, regular screening of high-risk groups irrespective of symptoms, and quarantine of contacts of laboratory-confirmed cases identified through test-and-trace protocols. The expected effectiveness of different testing strategies was defined as the percentage reduction in R. We reviewed data on the performance of antibody tests reported by the Foundation for Innovative New Diagnostics and examined their implications for the use of so-called immunity passports. FINDINGS: If all individuals with symptoms compatible with COVID-19 self-isolated and self-isolation was 100% effective in reducing onwards transmission, self-isolation of symptomatic individuals would result in a reduction in R of 47% (95% uncertainty interval [UI] 32-55). PCR testing to identify SARS-CoV-2 infection soon after symptom onset could reduce the number of individuals needing to self-isolate, but would also reduce the effectiveness of self-isolation (around 10% would be false negatives). Weekly screening of health-care workers and other high-risk groups irrespective of symptoms by use of PCR testing is estimated to reduce their contribution to SARS-CoV-2 transmission by 23% (95% UI 16-40), on top of reductions achieved by self-isolation following symptoms, assuming results are available at 24 h. The effectiveness of test and trace depends strongly on coverage and the timelines
Thompson H, Imai N, Dighe A, et al., 2020, SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China, Journal of Travel Medicine, Vol: 27, Pages: 1-3, ISSN: 1195-1982
We estimated SARS-CoV-2 infection prevalence in cohorts of repatriated citizens from Wuhan to be 0.44% (95% CI: 0.19%–1.03%). Although not representative of the wider population we believe these estimates are helpful in providing a conservative estimate of infection prevalence in Wuhan City, China, in the absence of large-scale population testing early in the epidemic.
Biggerstaff M, Cowling BJ, Cucunubá ZM, et al., 2020, Early insights from statistical and mathematical modeling of key epidemiologic parameters of COVID-19, Emerging Infectious Diseases, Vol: 26, ISSN: 1080-6040
We report key epidemiologic parameter estimates for coronavirus disease identified in peer-reviewed publications, preprint articles, and online reports. Range estimates for incubation period were 1.8–6.9 days, serial interval 4.0–7.5 days, and doubling time 2.3–7.4 days. The effective reproductive number varied widely, with reductions attributable to interventions. Case burden and infection fatality ratios increased with patient age. Implementation of combined interventions could reduce cases and delay epidemic peak up to 1 month. These parameters for transmission, disease severity, and intervention effectiveness are critical for guiding policy decisions. Estimates will likely change as new information becomes available.
Cucunubá ZM, 2020, Latin American scientific research prorities for COVID-19 prevention and control [Investigación científica prioritaria en Latinoamérica para orientar la prevención y el control de la COVID-19 ], Biomedica, Vol: 40, Pages: 9-13, ISSN: 0120-4157
Brazeau N, Verity R, Jenks S, et al., 2020, Report 34: COVID-19 infection fatality ratio: estimates from seroprevalence
The infection fatality ratio (IFR) is a key statistic for estimating the burden of coronavirus disease 2019 (COVID-19) and has been continuously debated throughout the current pandemic. Previous estimates have relied on data early in the epidemic, or have not fully accounted for uncertainty in serological test characteristics and delays from onset of infection to seroconversion, death, and antibody waning. After screening 175 studies, we identified 10 representative antibody surveys to obtain updated estimates of the IFR using a modelling framework that addresses the limitations listed above. We inferred serological test specificity from regional variation within serosurveys, which is critical for correctly estimating the cumulative proportion infected when seroprevalence is still low. We find that age-specific IFRs follow an approximately log-linear pattern, with the risk of death doubling approximately every eight years of age. Using these age-specific estimates, we estimate the overall IFR in a typical low-income country, with a population structure skewed towards younger individuals, to be 0.23% (0.14-0.42 95% prediction interval range). In contrast, in a typical high income country, with a greater concentration of elderly individuals, we estimate the overall IFR to be 1.15% (0.78-1.79 95% prediction interval range). We show that accounting for seroreversion, the waning of antibodies leading to a negative serological result, can slightly reduce the IFR among serosurveys conducted several months after the first wave of the outbreak, such as Italy. In contrast, uncertainty in test false positive rates combined with low seroprevalence in some surveys can reconcile apparently low crude fatality ratios with the IFR in other countries. Unbiased estimates of the IFR continue to be critical to policymakers to inform key response decisions. It will be important to continue to monitor the IFR as new treatments are introduced. The code for reproducing these results are av
Carrera J-P, Cucunubá ZM, Neira K, et al., 2020, Endemic and epidemic human alphavirus infections in eastern Panama: an analysis of population-based cross-sectional surveys., American Journal of Tropical Medicine and Hygiene, Vol: 103, Pages: 2429-2437, ISSN: 0002-9637
Madariaga virus (MADV) has recently been associated with severe human disease in Panama, where the closely related Venezuelan equine encephalitis virus (VEEV) also circulates. In June 2017, a fatal MADV infection was confirmed in a community of Darien Province. We conducted a cross-sectional outbreak investigation with human and mosquito collections in July 2017, where sera were tested for alphavirus antibodies and viral RNA. In addition, by applying a catalytic, force-of-infection (FOI) statistical model to two serosurveys from Darien Province in 2012 and 2017, we investigated whether endemic or epidemic alphavirus transmission occurred historically. In 2017, MADV and VEEV IgM seroprevalences were 1.6% and 4.4%, respectively; IgG antibody prevalences were MADV: 13.2%, VEEV: 16.8%, Una virus (UNAV): 16.0%, and Mayaro virus: 1.1%. Active viral circulation was not detected. Evidence of MADV and UNAV infection was found near households, raising questions about its vectors and enzootic transmission cycles. Insomnia was associated with MADV and VEEV infections, depression symptoms were associated with MADV, and dizziness with VEEV and UNAV. Force-of-infection analyses suggest endemic alphavirus transmission historically, with recent increased human exposure to MADV and VEEV in Aruza and Mercadeo, respectively. The lack of additional neurological cases suggests that severe MADV and VEEV infections occur only rarely. Our results indicate that over the past five decades, alphavirus infections have occurred at low levels in eastern Panama, but that MADV and VEEV infections have recently increased-potentially during the past decade. Endemic infections and outbreaks of MADV and VEEV appear to differ spatially in some locations of eastern Panama.
Dighe A, Cattarino L, Cuomo-Dannenburg G, et al., 2020, Response to COVID-19 in South Korea and implications for lifting stringent interventions, BMC Medicine, Vol: 18, Pages: 1-12, ISSN: 1741-7015
Background After experiencing a sharp growth in COVID-19 cases early in the pandemic, South Korea rapidly controlled transmission while implementing less stringent national social distancing measures than countries in Europe and the US. This has led to substantial interest in their “test, trace, isolate” strategy. However, it is important to understand the epidemiological peculiarities of South Korea’s outbreak and characterise their response before attempting to emulate these measures elsewhere.MethodsWe systematically extracted numbers of suspected cases tested, PCR-confirmed cases, deaths, isolated confirmed cases, and numbers of confirmed cases with an identified epidemiological link from publicly available data. We estimated the time-varying reproduction number, Rt, using an established Bayesian framework, and reviewed the package of interventions implemented by South Korea using our extracted data, plus published literature and government sources. Results We estimated that after the initial rapid growth in cases, Rt dropped below one in early April before increasing to a maximum of 1.94 (95%CrI; 1.64-2.27) in May following outbreaks in Seoul Metropolitan Region. By mid-June Rt was back below one where it remained until the end of our study (July 13th). Despite less stringent “lockdown” measures, strong social distancing measures were implemented in high incidence areas and studies measured a considerable national decrease in movement in late-February. Testing capacity was swiftly increased, and protocols were in place to isolate suspected and confirmed cases quickly however we could not estimate the delay to isolation using our data. Accounting for just 10% of cases, individual case-based contact-tracing picked up a relatively minor proportion of total cases, with cluster investigations accounting for 66%. ConclusionsWhilst early adoption of testing and contact-tracing are likely to be important for South Korea’s successf
Ainslie K, Walters C, Fu H, et al., 2020, Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment, Wellcome Open Research, ISSN: 2398-502X
Background : The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods : Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results : Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies.
Hogan A, Winskill P, Watson O, et al., 2020, Report 33: Modelling the allocation and impact of a COVID-19 vaccine
Several SARS-CoV-2 vaccine candidates are now in late-stage trials, with efficacy and safety results expected by the end of 2020. Even under optimistic scenarios for manufacture and delivery, the doses available in 2021 are likely to be limited. Here we identify optimal vaccine allocation strategies within and between countries to maximise health (avert deaths) under constraints on dose supply. We extended an existing mathematical model of SARS-CoV-2 transmission across different country settings to model the public health impact of potential vaccines, using a range of target product profiles developed by the World Health Organization. We show that as supply increases, vaccines that reduce or block infection – and thus transmission – in addition to preventing disease have a greater impact than those that prevent disease alone, due to the indirect protection provided to high-risk groups. We further demonstrate that the health impact of vaccination will depend on the cumulative infection incidence in the population when vaccination begins, the duration of any naturally acquired immunity, the likely trajectory of the epidemic in 2021 and the level of healthcare available to effectively treat those with disease. Within a country, we find that for a limited supply (doses for <20% of the population) the optimal strategy is to target the elderly and other high-risk groups. However, if a larger supply is available, the optimal strategy switches to targeting key transmitters (i.e. the working age population and potentially children) to indirectly protect the elderly and vulnerable. Given the likely global dose supply in 2021 (2 billion doses with a two-dose vaccine), we find that a strategy in which doses are allocated to countries in proportion to their population size is close to optimal in averting deaths. Such a strategy also aligns with the ethical principles agreed in pandemic preparedness planning.
Monod M, Blenkinsop A, Xi X, et al., 2020, Report 32: Targeting interventions to age groups that sustain COVID-19 transmission in the United States, Pages: 1-32
Following inial declines, in mid 2020, a resurgence in transmission of novel coronavirus disease (COVID-19) has occurred in the United States and parts of Europe. Despite the wide implementaon of non-pharmaceucal inter-venons, it is sll not known how they are impacted by changing contact paerns, age and other demographics. As COVID-19 disease control becomes more localised, understanding the age demographics driving transmission and how these impact the loosening of intervenons such as school reopening is crucial. Considering dynamics for the United States, we analyse aggregated, age-speciﬁc mobility trends from more than 10 million individuals and link these mechaniscally to age-speciﬁc COVID-19 mortality data. In contrast to previous approaches, we link mobility to mortality via age speciﬁc contact paerns and use this rich relaonship to reconstruct accurate trans-mission dynamics. Contrary to anecdotal evidence, we ﬁnd lile support for age-shis in contact and transmission dynamics over me. We esmate that, unl August, 63.4% [60.9%-65.5%] of SARS-CoV-2 infecons in the United States originated from adults aged 20-49, while 1.2% [0.8%-1.8%] originated from children aged 0-9. In areas with connued, community-wide transmission, our transmission model predicts that re-opening kindergartens and el-ementary schools could facilitate spread and lead to considerable excess COVID-19 aributable deaths over a 90-day period. These ﬁndings indicate that targeng intervenons to adults aged 20-49 are an important con-sideraon in halng resurgent epidemics, and prevenng COVID-19-aributable deaths when kindergartens and elementary schools reopen.
van Elsland S, Watson O, Alhaffar M, et al., 2020, Report 31: Estimating the burden of COVID-19 in Damascus, Syria: an analysis of novel data sources to infer mortality under-ascertainment
The COVID-19 pandemic has resulted in substantial mortality worldwide. However, to date, countries in the Middle East and Africa have reported substantially lower mortality rates than in Europe and the Americas. One hypothesis is that these countries have been ‘spared’, but another is that deaths have been under-ascertained (deaths that have been unreported due to any number of reasons, for instance due to limited testing capacity). However, the scale of under-ascertainment is difficult to assess with currently available data. In this analysis, we estimate the potential under-ascertainment of COVID-19 mortality in Damascus, Syria, where all-cause mortality data has been reported between 25th July and 1st August. We fit a mathematical model of COVID-19 transmission to reported COVID-19 deaths in Damascus since the beginning of the pandemic and compare the model-predicted deaths to reported excess deaths. Exploring a range of different assumptions about under-ascertainment, we estimate that only 1.25% of deaths (sensitivity range 1% - 3%) due to COVID-19 are reported in Damascus. Accounting for under-ascertainment also corroborates local reports of exceeded hospital bed capacity. To validate the epidemic dynamics inferred, we leverage community-uploaded obituary certificates as an alternative data source, which confirms extensive mortality under-ascertainment in Damascus between July and August. This level of under-ascertainment suggests that Damascus is at a much later stage in its epidemic than suggested by surveillance reports, which have repo. We estimate that 4,340 (95% CI: 3,250 - 5,540) deaths due to COVID-19 in Damascus may have been missed as of 2nd September 2020. Given that Damascus is likely to have the most robust surveillance in Syria, these findings suggest that other regions of the country could have experienced similar or worse mortality rates due to COVID-19.
Charniga K, Cucunubá Z, Mercado M, et al., 2020, Spatial and temporal invasion dynamics of the 2014-2017 Zika and chikungunya epidemics in Colombia, PLoS Computational Biology, ISSN: 1553-734X
Zika virus (ZIKV) and chikungunya virus (CHIKV) were recently introduced into the Americas resulting in significant disease burdens. Understanding their spatial and temporal dynamics at the subnational level is key to informing surveillance and preparedness for future epidemics. We analyzed anonymized line list data on approximately 105,000 Zika virus disease and 412,000 chikungunya fever suspected and laboratory-confirmed cases during the 2014-2017 epidemics. We first determined the week of invasion in each city. Out of 1,122, 288 cities met criteria for epidemic invasion by ZIKA and 338 cities by CHIKV. We estimated that the geographic origin of both epidemics was located in Barranquilla, north Colombia. Using gravity models, we assessed the spatial and temporal invasion dynamics of both viruses to analyze transmission between cities. Invasion risk was best captured when accounting for geographic distance and intermediate levels of density dependence. Although a few long-distance invasion events occurred at the beginning of the epidemics, an estimated distance power of 1.7 (95% CrI: 1.5-2.0) suggests that spatial spread was primarily driven by short-distance transmission. Cities with large populations were more likely to spread disease than cities with smaller populations. Similarities between the epidemics included having the same estimated geographic origin and having the same five parameters estimated in the best-fitting models. ZIKV spread considerably faster than CHIKV. <h4>Author summary</h4> Understanding the spread of infectious diseases across space and time is critical for preparedness, designing interventions, and elucidating mechanisms underlying transmission. We analyzed human case data from over 500,000 reported cases to investigate the spread of the recent Zika virus (ZIKV) and chikungunya virus (CHIKV) epidemics in Colombia. Both viruses were introduced into northern Colombia. We found that intermediate levels of density dependence best
Lavezzo E, Franchin E, Ciavarella C, et al., 2020, Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo', Nature, Vol: 584, Pages: 425-429, ISSN: 0028-0836
On the 21st of February 2020 a resident of the municipality of Vo', a small town near Padua, died of pneumonia due to SARS-CoV-2 infection1. This was the first COVID-19 death detected in Italy since the emergence of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. We collected information on the demography, clinical presentation, hospitalization, contact network and presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. On the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI) 2.1-3.3%). On the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% Confidence Interval (CI) 0.8-1.8%). Notably, 42.5% (95% CI 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (i.e. did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (p-values 0.62 and 0.74 for E and RdRp genes, respectively, Exact Wilcoxon-Mann-Whitney test). This study sheds new light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides new insights into its transmission dynamics and the efficacy of the implemented control measures.
Vecino-Ortiz A, Villanueva Congote J, Zapata Bedoya S, et al., 2020, Impact of contact tracing on COVID-19 mortality: An impact evaluation using surveillance data from Colombia, PLoS One, ISSN: 1932-6203
<h4>Background</h4> Contact tracing is a key part of the public health surveillance toolkit. However, it is labor intensive and costly to carry it out. Some countries have faced challenges implementing contact tracing, and no impact evaluations to our knowledge have assessed its impact on COVID-19 mortality. This study assesses the impact of contact tracing in a middle-income country and provides data to support the expansion of contact tracing strategies with the aim of improving infection control. <h4>Methods</h4> We obtained publicly available data on all confirmed COVID-19 cases in Colombia between March 2 and June 16, 2020. (N=54,931 cases over 135 days of observation). We proxied contact tracing performance as the proportion of cases identified through contact tracing out of all cases identified, as suggested by WHO guidelines. We calculated the daily proportion of cases identified through contact tracing across 37 geographical units (32 departments and five districts). Further, we used a sequential log-log fixed-effects model to estimate the 21-days, 28-days, 42-days and 56-days lagged impact of the proportion of cases identified through contact tracing on the daily number of COVID-19 deaths. Both the proportion of cases identified through contact tracing and the daily number of COVID-19 deaths are smoothed using 7-day moving averages. Models control for prevalence of active cases, second-degree polynomials, and mobility indices. Robustness checks to include supply-side variables were performed. <h4>Results</h4> We found that a 10 percent increase in the proportion of cases identified through contact tracing is related to COVID-19 mortality reductions between 0.8% and 3.4%. Our models explain between 47%-70% of the variance in mortality. Results are robust to changes of specification and inclusion of supply-side variables. <h4>Conclusion</h4> Contact tracing is instrumental to contain infectious diseases and its
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